Fig. 5

Evaluate SMARTcleaner with a TF ChIP-seq data. a An example of false peaks in the original list of Olig2 ChIP-seq peaks. The track of “called peak” shows peaks provided by the authors. b Venn diagram showing the peak overlaps from three methods: the original peaks from the authors, the peaks called before cleaning, and the peaks called after cleaning. When counting the overlapping peaks, we could get two different numbers depending on which set of peaks is used to report the number (one peak in one set may overlap more than one peak in another set). We reported the smaller number here. c Peaks overlapping with poly(T/A) sites. d, e Read densities and average counts at the four selected groups of peaks, computed by sampling 5 million reads. An Olig2 ChIP-seq data (right) from non-SMART method was also analyzed. f Top enriched motifs by HOMER [30]